
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   64 (   64),  selected   60 , name T0316TS393_5-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316TS393_5-D2.T0316_D2.pdb  -3  -ie  -o1  -sda  -d:4  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25       247 - 275         4.87     9.85
  LONGEST_CONTINUOUS_SEGMENT:    25       248 - 276         4.89     9.84
  LONGEST_CONTINUOUS_SEGMENT:    25       259 - 283         4.87    10.44
  LCS_AVERAGE:     35.72

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       251 - 264         1.74    12.82
  LCS_AVERAGE:     11.94

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       232 - 236         0.72    20.80
  LONGEST_CONTINUOUS_SEGMENT:     5       262 - 266         0.98    11.52
  LONGEST_CONTINUOUS_SEGMENT:     5       272 - 276         0.64    12.06
  LCS_AVERAGE:      6.92

LCS_GDT    MOLECULE-1    MOLECULE-2    LENGTH_OF_THE
LCS_GDT     RESIDUE       RESIDUE         CONTINUOUS
LCS_GDT   NAME NUMBER   NAME NUMBER          SEGMENT     GLOBAL DISTANCE TEST - GDT_DATA_COLUMNS                             NUMBER OF THE RESIDUES:   60
LCS_GDT     G     220     G     220      4    6   11     3    4    4    5   10   12   15   16   18   18   19   21   23   25   31   33   36   38   40   43 
LCS_GDT     R     221     R     221      4    6   11     3    4    4    5    5   12   15   16   18   18   19   21   23   29   31   33   36   38   40   44 
LCS_GDT     M     222     M     222      4    6   16     3    4   10   10   11   13   15   16   18   19   21   23   25   30   35   37   42   42   45   46 
LCS_GDT     M     223     M     223      4    6   16     3    4    5    7    8   12   13   16   18   18   20   21   25   29   33   36   39   42   45   46 
LCS_GDT     T     224     T     224      4    7   16     2    4    5    6    8    8   10   11   13   15   17   19   20   22   28   29   33   35   39   42 
LCS_GDT     V     225     V     225      4    7   16     3    4    5    6    8    8   10   11   13   13   15   17   20   21   23   25   27   30   31   32 
LCS_GDT     D     226     D     226      4    7   16     3    4    5    6    8    8   10   11   13   13   16   17   20   21   23   25   27   30   31   32 
LCS_GDT     G     227     G     227      4    7   16     3    4    5    7    8   10   10   11   13   14   16   18   20   21   23   25   27   30   31   35 
LCS_GDT     R     228     R     228      4    8   16     3    3    5    7    8   11   12   15   16   18   19   19   20   23   28   30   32   35   38   40 
LCS_GDT     D     229     D     229      4    8   16     3    4   10   10   11   13   15   16   18   19   20   22   25   29   33   36   39   42   45   46 
LCS_GDT     M     230     M     230      4    8   16     2    4    6    7    8    9   15   15   17   19   21   23   29   32   37   40   42   42   45   46 
LCS_GDT     G     231     G     231      4    8   17     3    4    6    7    8   11   14   16   21   24   27   31   34   35   37   40   42   42   45   46 
LCS_GDT     E     232     E     232      5    8   18     4    4    6    7    8   11   13   17   22   25   27   31   34   35   37   40   42   42   45   46 
LCS_GDT     H     233     H     233      5    8   18     4    4    6    8    9   10   15   17   22   25   27   31   34   35   37   39   40   42   44   45 
LCS_GDT     A     234     A     234      5    8   18     4    4    6    7    8    9   13   16   17   20   22   25   27   29   33   34   35   38   40   41 
LCS_GDT     G     235     G     235      5    8   18     4    6    6    7    8   11   13   16   17   19   20   21   25   26   29   32   35   38   40   41 
LCS_GDT     L     236     L     236      5    6   18     3    4    5    6    8    8   10   11   14   14   19   21   25   27   32   34   35   38   40   41 
LCS_GDT     M     237     M     237      3    5   18     0    6    6    6    6   11   13   16   17   19   20   21   25   26   28   32   35   38   40   41 
LCS_GDT     Y     238     Y     238      4    6   18     3    3    4    6    8   11   13   16   17   19   22   25   27   32   33   34   36   38   40   41 
LCS_GDT     Y     239     Y     239      4    6   18     3    3    4    5    8    9   13   17   22   25   27   31   34   35   37   40   42   42   45   46 
LCS_GDT     T     240     T     240      4    6   18     3    4    5    8    9   11   15   17   22   25   27   31   34   35   37   40   42   42   45   46 
LCS_GDT     I     241     I     241      4    6   18     3    4    4    6    8   11   13   17   22   25   27   31   34   35   37   40   42   42   45   46 
LCS_GDT     G     242     G     242      4    6   18     3    4    4    6    8   11   13   16   18   24   24   28   32   35   37   39   42   42   45   46 
LCS_GDT     Q     243     Q     243      4    6   20     3    4    4    6    8   11   13   17   22   25   27   31   34   35   37   40   42   42   45   46 
LCS_GDT     R     244     R     244      4    4   20     3    4    5    5    6    8   13   17   22   25   27   31   34   35   37   40   42   42   45   46 
LCS_GDT     G     245     G     245      4    4   20     3    4    5    5    6    8   13   17   22   25   27   31   34   35   37   40   42   42   45   46 
LCS_GDT     G     246     G     246      3    5   20     3    4    5    5    6   10   13   17   22   25   27   31   34   35   37   39   40   42   45   46 
LCS_GDT     L     247     L     247      4    5   25     3    3    4    5    6    8   12   17   22   25   27   31   34   35   37   40   42   42   45   46 
LCS_GDT     G     248     G     248      4    5   25     3    6    6    7    8   11   14   16   21   24   27   31   34   35   37   40   42   42   45   46 
LCS_GDT     I     249     I     249      4    5   25     3    3    5    7    9   11   15   16   18   23   27   29   32   35   37   40   42   42   45   46 
LCS_GDT     G     250     G     250      4    6   25     3    3    4    9   11   13   15   16   18   20   21   23   27   32   36   40   42   42   45   46 
LCS_GDT     G     251     G     251      4   10   25     3    3    5    8   10   13   15   16   18   20   21   23   27   32   36   40   42   42   45   46 
LCS_GDT     D     256     D     256      4   10   25     3    4    5    7   11   13   15   16   18   20   23   27   31   34   37   40   42   42   45   46 
LCS_GDT     N     257     N     257      4   10   25     3    4   10   10   11   13   15   16   18   23   27   29   32   35   37   40   42   42   45   46 
LCS_GDT     A     258     A     258      4   10   25     3    6   10   10   11   13   15   16   18   23   27   29   32   35   37   40   42   42   45   46 
LCS_GDT     P     259     P     259      4   10   25     4    6   10   10   11   13   15   16   21   25   27   31   34   35   37   40   42   42   45   46 
LCS_GDT     W     260     W     260      4   10   25     4    6    6    6   11   13   15   16   21   24   27   31   34   35   37   40   42   42   45   46 
LCS_GDT     F     261     F     261      4   10   25     4    6   10   10   11   13   15   16   22   25   27   31   34   35   37   40   42   42   45   46 
LCS_GDT     V     262     V     262      5   10   25     4    6   10   10   11   13   15   16   19   24   27   31   34   35   37   40   42   42   45   46 
LCS_GDT     V     263     V     263      5   10   25     3    6   10   10   11   13   15   17   22   25   27   31   34   35   37   40   42   42   45   46 
LCS_GDT     G     264     G     264      5   10   25     3    6   10   10   11   13   15   17   22   25   27   31   34   35   37   40   42   42   45   46 
LCS_GDT     K     265     K     265      5    8   25     3    6    6    7    8   11   15   17   22   25   27   31   34   35   37   40   42   42   45   46 
LCS_GDT     D     266     D     266      5    8   25     3    5    6    7    8   11   15   17   22   25   27   31   34   35   37   40   42   42   45   46 
LCS_GDT     L     267     L     267      4    8   25     2    5    6    6    8   11   15   17   21   25   27   31   34   35   37   40   42   42   45   46 
LCS_GDT     S     268     S     268      4    8   25     3    4    6    6    8   10   15   17   20   21   23   29   34   35   37   40   42   42   45   46 
LCS_GDT     K     269     K     269      3    8   25     3    3    4    5    6   11   15   17   20   21   24   30   34   35   37   40   42   42   45   46 
LCS_GDT     N     270     N     270      3    7   25     3    3    4    5    9   10   14   17   22   25   27   31   34   35   37   40   42   42   45   46 
LCS_GDT     I     271     I     271      3    8   25     3    4    6    8    9   11   15   17   22   25   27   31   34   35   37   40   42   42   45   46 
LCS_GDT     L     272     L     272      5    8   25     3    5    5    8    9   11   15   17   22   25   27   31   34   35   37   40   42   42   45   46 
LCS_GDT     Y     273     Y     273      5    8   25     3    5    6    8    9   11   15   17   22   25   27   31   34   35   37   40   42   42   45   46 
LCS_GDT     V     274     V     274      5    8   25     3    5    6    8    9   11   15   17   22   25   27   31   34   35   37   40   42   42   45   46 
LCS_GDT     G     275     G     275      5    8   25     3    5    6    8    9   11   15   17   22   25   27   31   34   35   37   40   42   42   45   46 
LCS_GDT     Q     276     Q     276      5    8   25     3    5    6    8    9   10   15   17   21   25   27   31   34   35   37   40   42   42   45   46 
LCS_GDT     G     277     G     277      4    8   25     3    4    5    6    8   11   15   17   20   20   22   26   32   33   36   38   41   42   45   46 
LCS_GDT     F     278     F     278      4    8   25     3    4    5    6    8   11   13   16   20   20   22   25   27   30   33   36   41   41   44   46 
LCS_GDT     Y     279     Y     279      3    5   25     3    3    3    4    5   10   15   17   20   20   23   30   34   35   37   40   42   42   45   46 
LCS_GDT     H     280     H     280      4    5   25     4    6    6    6    6    9   13   16   22   25   27   31   34   35   37   40   42   42   45   46 
LCS_GDT     D     281     D     281      4    4   25     4    6    6    6    6    8   13   16   22   25   27   31   34   35   37   40   42   42   45   46 
LCS_GDT     S     282     S     282      4    4   25     4    6    6    6    6    7   13   16   21   25   27   31   34   35   37   40   42   42   45   46 
LCS_GDT     L     283     L     283      4    4   25     4    6   10   10   11   13   15   17   22   25   27   31   34   35   37   40   42   42   45   46 
LCS_AVERAGE  LCS_A:  18.19  (   6.92   11.94   35.72 )

GLOBAL_DISTANCE_TEST (the largest set of residues that can fit under specified DISTANCE_CUTOFF)
GDT DIST_CUTOFF  0.50   1.00   1.50   2.00   2.50   3.00   3.50   4.00   4.50   5.00   5.50   6.00   6.50   7.00   7.50   8.00   8.50   9.00   9.50  10.00
GDT NUMBER_CA      4      6     10     10     11     13     15     17     22     25     27     31     34     35     37     40     42     42     45     46 
GDT PERCENT_CA   6.67  10.00  16.67  16.67  18.33  21.67  25.00  28.33  36.67  41.67  45.00  51.67  56.67  58.33  61.67  66.67  70.00  70.00  75.00  76.67
GDT RMS_LOCAL    0.31   0.52   1.25   1.25   1.51   1.82   2.13   3.00   3.49   3.68   3.83   4.28   4.64   4.65   4.90   5.54   5.75   5.71   6.22   6.31
GDT RMS_ALL_CA  17.85  16.54  11.87  11.87  11.91  11.95  12.14  12.00  11.09  10.97  10.91  10.58  10.30  10.38  10.24   9.86   9.84   9.89   9.79   9.79

#      Molecule1      Molecule2       DISTANCE
LGA    G     220      G     220         19.594
LGA    R     221      R     221         17.667
LGA    M     222      M     222         13.588
LGA    M     223      M     223         15.162
LGA    T     224      T     224         19.244
LGA    V     225      V     225         23.476
LGA    D     226      D     226         26.713
LGA    G     227      G     227         23.097
LGA    R     228      R     228         22.039
LGA    D     229      D     229         16.376
LGA    M     230      M     230         12.757
LGA    G     231      G     231          9.001
LGA    E     232      E     232          3.899
LGA    H     233      H     233          3.359
LGA    A     234      A     234          9.270
LGA    G     235      G     235         11.997
LGA    L     236      L     236         11.568
LGA    M     237      M     237         11.907
LGA    Y     238      Y     238          7.880
LGA    Y     239      Y     239          5.613
LGA    T     240      T     240          3.701
LGA    I     241      I     241          5.971
LGA    G     242      G     242         11.016
LGA    Q     243      Q     243          7.150
LGA    R     244      R     244          9.158
LGA    G     245      G     245          8.454
LGA    G     246      G     246          5.784
LGA    L     247      L     247          7.947
LGA    G     248      G     248         11.704
LGA    I     249      I     249         14.411
LGA    G     250      G     250         20.509
LGA    G     251      G     251         19.490
LGA    D     256      D     256         22.957
LGA    N     257      N     257         20.388
LGA    A     258      A     258         16.437
LGA    P     259      P     259         12.730
LGA    W     260      W     260         12.052
LGA    F     261      F     261          9.026
LGA    V     262      V     262          8.362
LGA    V     263      V     263          5.881
LGA    G     264      G     264          4.302
LGA    K     265      K     265          4.011
LGA    D     266      D     266          2.633
LGA    L     267      L     267          2.410
LGA    S     268      S     268          3.409
LGA    K     269      K     269          3.235
LGA    N     270      N     270          3.977
LGA    I     271      I     271          2.636
LGA    L     272      L     272          2.636
LGA    Y     273      Y     273          1.923
LGA    V     274      V     274          1.576
LGA    G     275      G     275          2.066
LGA    Q     276      Q     276          2.898
LGA    G     277      G     277          3.197
LGA    F     278      F     278          4.731
LGA    Y     279      Y     279          3.960
LGA    H     280      H     280          7.214
LGA    D     281      D     281          8.320
LGA    S     282      S     282          7.299
LGA    L     283      L     283          3.968

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   64   60    4.0     17    3.00    30.417    26.488     0.549

LGA_LOCAL      RMSD =  2.997  Number of atoms =   17  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.961  Number of atoms =   60 
Std_ALL_ATOMS  RMSD =  9.765  (standard rmsd on all 60 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.392058 * X  +  -0.096587 * Y  +  -0.914856 * Z  +  35.725384
  Y_new =   0.918119 * X  +  -0.103639 * Y  +  -0.382514 * Z  +  16.516619
  Z_new =  -0.057869 * X  +  -0.989914 * Y  +   0.129311 * Z  + -13.170813 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.440903    1.700689  [ DEG:   -82.5577     97.4423 ]
  Theta =   0.057901    3.083692  [ DEG:     3.3175    176.6825 ]
  Phi   =   1.974379   -1.167213  [ DEG:   113.1236    -66.8764 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0316TS393_5-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS393_5-D2.T0316_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   64   60   4.0   17   3.00  26.488     9.77
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS393_5-D2
PFRMAT TS
TARGET T0316
MODEL 5
PARENT N/A
ATOM    220  CA  GLY   220      38.052  16.475  -3.391  1.00 25.00           C
ATOM    221  CA  ARG   221      38.117  18.564  -6.623  1.00 25.00           C
ATOM    222  CA  MET   222      38.649  18.134 -10.379  1.00 25.00           C
ATOM    223  CA  MET   223      41.314  20.765 -11.253  1.00 25.00           C
ATOM    224  CA  THR   224      44.250  23.081 -11.651  1.00 25.00           C
ATOM    225  CA  VAL   225      44.131  24.188  -8.062  1.00 25.00           C
ATOM    226  CA  ASP   226      41.368  22.739  -5.815  1.00 25.00           C
ATOM    227  CA  GLY   227      42.771  19.456  -7.153  1.00 25.00           C
ATOM    228  CA  ARG   228      44.763  18.318 -10.187  1.00 25.00           C
ATOM    229  CA  ASP   229      44.350  19.163 -13.857  1.00 25.00           C
ATOM    230  CA  MET   230      43.275  20.117 -17.385  1.00 25.00           C
ATOM    231  CA  GLY   231      42.634  23.541 -18.804  1.00 25.00           C
ATOM    232  CA  GLU   232      42.001  26.711 -20.700  1.00 25.00           C
ATOM    233  CA  HIS   233      41.896  24.378 -23.694  1.00 25.00           C
ATOM    234  CA  ALA   234      39.917  25.491 -26.798  1.00 25.00           C
ATOM    235  CA  GLY   235      38.000  22.288 -26.160  1.00 25.00           C
ATOM    236  CA  LEU   236      40.442  19.440 -25.478  1.00 25.00           C
ATOM    237  CA  MET   237      38.903  20.568 -22.191  1.00 25.00           C
ATOM    238  CA  TYR   238      37.793  21.888 -18.798  1.00 25.00           C
ATOM    239  CA  TYR   239      38.653  20.172 -15.577  1.00 25.00           C
ATOM    240  CA  THR   240      36.489  21.469 -12.724  1.00 25.00           C
ATOM    241  CA  ILE   241      34.939  21.644  -9.204  1.00 25.00           C
ATOM    242  CA  GLY   242      34.512  24.310  -6.588  1.00 25.00           C
ATOM    243  CA  GLN   243      32.799  26.289  -9.322  1.00 25.00           C
ATOM    244  CA  ARG   244      34.867  25.864 -12.483  1.00 25.00           C
ATOM    245  CA  GLY   245      36.696  28.407 -14.597  1.00 25.00           C
ATOM    246  CA  GLY   246      38.308  26.394 -17.298  1.00 25.00           C
ATOM    247  CA  LEU   247      40.004  24.371 -14.602  1.00 25.00           C
ATOM    248  CA  GLY   248      41.009  26.891 -11.936  1.00 25.00           C
ATOM    249  CA  ILE   249      38.969  24.257 -10.053  1.00 25.00           C
ATOM    250  CA  GLY   250      39.052  26.469  -6.907  1.00 25.00           C
ATOM    251  CA  GLY   251      36.799  28.896  -8.777  1.00 25.00           C
ATOM    252  CA  GLN   252      39.017  31.391 -10.604  1.00 25.00           C
ATOM    253  CA  HIS   253      40.680  33.996 -12.812  1.00 25.00           C
ATOM    254  CA  GLY   254      42.479  34.127 -16.185  1.00 25.00           C
ATOM    255  CA  GLY   255      39.118  33.788 -17.866  1.00 25.00           C
ATOM    256  CA  ASP   256      37.109  36.417 -16.012  1.00 25.00           C
ATOM    257  CA  ASN   257      34.247  35.101 -13.869  1.00 25.00           C
ATOM    258  CA  ALA   258      33.019  31.778 -15.349  1.00 25.00           C
ATOM    259  CA  PRO   259      31.534  28.921 -13.396  1.00 25.00           C
ATOM    260  CA  TRP   260      28.821  26.972 -11.587  1.00 25.00           C
ATOM    261  CA  PHE   261      29.717  23.284 -10.993  1.00 25.00           C
ATOM    262  CA  VAL   262      28.604  19.719 -10.274  1.00 25.00           C
ATOM    263  CA  VAL   263      28.078  16.904 -12.814  1.00 25.00           C
ATOM    264  CA  GLY   264      30.728  14.327 -13.713  1.00 25.00           C
ATOM    265  CA  LYS   265      34.021  13.230 -15.300  1.00 25.00           C
ATOM    266  CA  ASP   266      37.561  13.996 -16.315  1.00 25.00           C
ATOM    267  CA  LEU   267      40.706  15.590 -14.947  1.00 25.00           C
ATOM    268  CA  SER   268      43.962  15.106 -16.913  1.00 25.00           C
ATOM    269  CA  LYS   269      46.588  16.715 -19.034  1.00 25.00           C
ATOM    270  CA  ASN   270      44.136  17.430 -21.843  1.00 25.00           C
ATOM    271  CA  ILE   271      41.014  15.279 -21.809  1.00 25.00           C
ATOM    272  CA  LEU   272      40.022  17.528 -18.891  1.00 25.00           C
ATOM    273  CA  TYR   273      36.339  17.613 -19.790  1.00 25.00           C
ATOM    274  CA  VAL   274      33.628  19.328 -21.825  1.00 25.00           C
ATOM    275  CA  GLY   275      30.012  18.360 -22.331  1.00 25.00           C
ATOM    276  CA  GLN   276      27.653  21.237 -22.981  1.00 25.00           C
ATOM    277  CA  GLY   277      24.751  19.715 -24.851  1.00 25.00           C
ATOM    278  CA  PHE   278      21.478  18.366 -23.415  1.00 25.00           C
ATOM    279  CA  TYR   279      18.388  19.081 -21.295  1.00 25.00           C
ATOM    280  CA  HIS   280      18.726  19.496 -17.513  1.00 25.00           C
ATOM    281  CA  ASP   281      17.642  15.918 -16.700  1.00 25.00           C
ATOM    282  CA  SER   282      20.870  15.508 -18.720  1.00 25.00           C
ATOM    283  CA  LEU   283      22.902  16.955 -15.814  1.00 25.00           C
TER
END
